Research workbench
Cryo-EM structure of the APE4 and NBR1 complex
Analyse Cryo-EM structure of the APE4 and NBR1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DDE
- Type
- protein
- Length
- 6,300 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl aminopeptidase 1,ZZ-type zinc finger-containing protein…
- EC
- 3.4.11.21
- UniProt
- O36014, Q9P792
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, V, X | Aspartyl aminopeptidase 1,ZZ-type zinc finger-containing protein P35G2.11C,MALTOSE/MALTODEXTRIN-binding periplasmic protein (EC 3.4.11.21) | protein | 525 | 26% helix, 27% strand | O36014, Q9P792 |
Ligands and binding sites
- ZN · Zinc ion · metal · 48 copies · chains A, C, E, X, G, I, K, M, O, Q, S, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.84 | 0.85 | 88 | empty |
| 2 | 1006 | 0.83 | 0.84 | 86 | empty |
| 3 | 941 | 0.83 | 0.85 | 80 | empty |
| 4 | 1025 | 0.83 | 0.84 | 87 | empty |
| 5 | 201 | 0.80 | 0.94 | 65 | empty |
Interfaces
18 interfaces between chains.
- G–M · 4638 Ų buried · 80 hydrogen bonds · protein-protein
- Q–S · 4591 Ų buried · 77 hydrogen bonds · protein-protein
- E–X · 4574 Ų buried · 72 hydrogen bonds · protein-protein
- I–K · 4570 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 4568 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 7DDE · Cryo-EM structure of the Ape4 and Nbr1 complex · the same entry in another collection · chain S against S, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O36014
- Every structure of UniProt Q9P792
- Elsewhere: RCSB PDB 7DDE · PDBe 7DDE · UniProt O36014 · UniProt Q9P792
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